Pokémon Mystery Dungeon: Clouds of Dusk
by Barimoss18
Summary: What starts off for Luke the Mudkip as an escape from proposing to his betrothed (with a Charmander-human by his side to boot) turns into a quest of self-discovery. This world may seem fresh and new, but it holds many dark secrets, including the very existence of Pokémon themselves.
1. Prologue: Creation

_Prologue: Creation_

In the beginning, there was nothing.

From nothing, the Original One created the universe.

He created three Forces: Time, Space, and Antimatter.

He created three forces: Knowledge, Emotion, and Willpower.

He created many other forces, such as Land, Sea, and Sky; Truth, Ideals, and Emptiness; Life, Death, and Order.

He created the planets and the stars.

From his thousand arms, He formed our world.

In the beginning, there was nothing.

The Original One formed everything from nothing.

But it was never told how much He created and, more importantly, how much He did not.

For it was what He did not create that led to Chaos.


	2. Chapter 1: Luke's Home

_Chapter 1:_

Falling, screaming, terror.

 _The cold._

 _So...cold..._

Silence.

The sun set on the ocean shore. The water vacillated up and down against the sand in small waves. The light from the sun, angling off the moving waters of the sea, created vibrant pinks and purples in the sky as it turned to dusk. This was why several Pokémon species had built their communities on the beach, including a clan of Mudkip.

Luke the Mudkip enjoyed this view. Every day before sunset, he'd venture toward and climb to the top of Pelipper's Perch to watch the sun create paintings more beautiful than the fabled auroras that were said to appear in the Arctic skies. Pelipper's Perch was a large isolated bluff, about forty feet tall, on the border between the beach and the forest behind it. This was where Mudkip was born, where he played as a young Kippling, where he had his first kiss. It was a special place for him.

On one somewhat foreboding night, Luke climbed up the bluff to admire the view as normal, albeit with some anxiousness bubbling inside. Sights like this made him love his home. The Wingull in the air had friendly conversations with each other. The rustling of the trees behind him merged with the soft crashing of the occasional larger wave on the sand in front of him to form a layer of quiet white noise on every side of him. Everything about it was soothing, relaxing, like Luke could forget the world and just exist in the moment. Whenever he felt stressed or depressed, he could just come up and wait for the sun to sink into the sea. It was easier to pretend like nothing else exists when he absorbed himself into the grand picture of the beach before him. Like this night.

The following day, Luke would turn 18. What would typically be a very happy day was fraught with worry. He would be accepted into the clan as a mature Pokémon and be given all of the privileges and responsibilities of one. He would also propose to his best friend, Ampers, who his parents had recently betrothed him to. They were inseparable in the community, but Luke could never see Ampers in that way. And vice versa. Besides, Luke had always loved the life he was living now: happy, carefree, and immune to the stress and duties of adulthood. He didn't want his age to change how he lived, but he had no choice in the matter.

He cursed this sunset. If it were less beautiful, maybe he wouldn't be so attached to his home. He would've ran away the second he was betrothed if he didn't love the beach. But the beach had given Luke so much joy over the years. He feared that he would be stuck here forever, living an unhappy life with someone he doesn't love.

He looked behind him towards the forest. "Maybe I should run," he muttered to himself. "It would be better off that way." But he didn't run. Maybe it was because of his attachment to home. Maybe it was because he didn't want to disappoint his parents. Maybe it was because everyone else was so excited for when they became an adult and he should have been too. Maybe it was because he was afraid of what living in the wild would bring to him.

Or maybe it was because of the Mystery Dungeons.

Every young Pokemon was taught about the Mystery Dungeons. They're areas full of feral Pokémon who have lost all civility and intelligence. They appear in random locations, and it's sometimes hard to tell if you've entered one or not. But the Mystery Dungeons are dangerous. The wild Pokémon can hurt you, yes, but they're constantly changing layout. The hallways and rooms are always moving, making it nearly impossible for a normal Pokémon to navigate.

The entire beach was surrounded by a forest. Some of that forest was a Mystery Dungeon, although Luke didn't know where exactly the Mystery Dungeon was or how dangerous the Pokémon inside of it were. Most Pokémon traveled solely along the beach to avoid wandering into it by accident.

It was in this moment that Luke resigned to his fate. He knew there was nothing he could do to prevent this from happening. Objecting to the ceremony and to proposing to his betrothed might as well make him feral. He'd be shunned from the community, probably being forced into the forest and possibly the Mystery Dungeon. He'd rather die.

He could die...

No. That was going way too far. He could never do that.

Maybe he was just hungry. He hadn't eaten in nearly two days from anxiety. He hadn't slept much either.

He looked away from the forest. It was time to head back home and eat something. Mom had said earlier she was making his favorite Lum Berry stew to celebrate his (too quickly approaching) big day.

He looked at the sunset one more time. One last time. It really was gorgeous. Maybe his new life wouldn't be so bad if he could see this every night, the stars beginning to peek out through the colors, the faint light on the ocean shore, the...

Wait a second. That light wasn't normally there. There was something attached to it.

It looked like a Pokémon!

Luke needed to check this out. That Pokémon might be in trouble!

He rushed down the bluff and across the beach towards the light. The light grew brighter as he approached, and it was clear that there was an orange Pokémon next to it. Or connected to it, or whatever. There was a Pokémon sleeping on the beach and there was a light. What was this?

Luke made it to the Pokémon, and its tail was ON FIRE. He screamed; he'd never seen a fire before (besides the flames his mother used to cook dinner). The warmth was nice, but it was fire. And this Pokémon was burning! He opened his mouth wide and forced a stream of water onto the flaming tail.

The Pokémon's eyes flashed open.

"AAAAEEEAAAAEEEOOOOOOOOAAAAAEEEEEEEE!"

The Pokémon leapt up and grabbed his tail in pain. He hopped up and down and cradled his tail as the flame went down slightly.

"Stay still, lemme finish putting you out!" Luke hollered above the wails of pain, startled by the other Pokémon's sudden transformation from lifeless lump into screaming banshee.

At this point, Luke gave the second Pokémon an actual look. He was bipedal, standing a head above the tip of his headfin. He was lizard-like in appearance, with an orange body and a cream belly. His tail had a flame on its tip, and Luke immediately realized his mistake.

"Oh, I'm so sorry!" Luke apologized. "I saw you passed out and a fire and I didn't realize it was just your tail."

The Charmander looked at him oddly. Then he looked at his tail. His eyes widened.

"Wait, what the heck...? Why do I have a tail?" He looked at Luke. His eyes widened further than what was probably healthy. "Y-y-y-you're a Mudkip..." he muttered. "H-how can you talk? How is this happening?"

Luke seemed confused. "Yeah, I'm a Mudkip. Always have been, always will. And you're a Charmander, although I don't know about your stance on evolution so I won't speak for you." He chuckled a little, but the Charmander didn't seem amused. He lifted up his arms. He saw orange hands and small claws. He ran to the water and peered at his reflection. The lizard Pokémon gasped and slowly backed away from the sea.

"I'm...a Charmander..." he said under his breath, in absolute shock.

"Well, yeah, duh," Luke responded. "What else did you expect to be? We don't change species in our sleep, you know?"

"But I'm not a Charmander!" the Charmander said. "I'm a human! I...I don't know what happened. You have to believe me."

At the word 'human', Luke tilted his head. "Human? You don't look like a human. And I'm pretty sure humans don't have flaming tails."

"I AM human!" the Charmander-human replied. "Please! I have no idea what's going on."

Luke thought to himself for a second, then said, "If you say you're a human, I believe you."

The Charmander looked surprised. "Y-you do?"

"Yeah, I see no reason not to. I've never met a human before, so I wouldn't know. They're the stuff of legend, so maybe they could turn into Pokémon or something."

The Charmander stood in silence. He and Luke stared at each other for a few seconds.

Luke cleared his throat. "So...uh...hi, I'm Luke. What's your name?"

The Charmander opened his mouth to answer, but stopped. "I...I don't remember. Gimme a second."

Luke almost questioned further but decided to let the Charmander think. Maybe memory loss was a part of being human. Or maybe the Charmander hit his head really hard. Asking about it wasn't going to make Charmander remember any faster.

Charmander, not appearing certain of anything, said, "I remember the name 'Theo', but I don't know if it's mine. I don't remember anything else, so I think that's my name."

"So we'll just call you Theo until you remember your name or something," Luke said. "What do you wanna do? You're a Pokémon right now, so you must be here for something."

"I don't know," Theo said. "I don't remember anything except that I'm human." He looked around. "This is too much for me. Maybe I'm dreaming."

"I don't think so," Luke said. "Otherwise, my Water Gun would've shocked you out of it before you even woke up here. I think." He thought for a second, then spoke again, "Besides, it'd kinda stink for my entire life to just be someone else's dream., right?"

Theo sat down, frustrated. "I just want to go home. I don't want to be a Pokémon!"

Luke said, "I can take you back to my home, if you want. We can give you food and shelter for a bit while you figure out what you want to do."

Theo nodded. "Thank you so much. I really appreciate this."

"No problem. The clan is just a small walk down the beach. Follow me."

Luke started walking, with Theo close behind him. Luke walked very lightly, happy and amazed to have met a human. Theo trod more heavily, confused and amazed to have become a Pokémon.

"So," Luke said, "you really remember nothing?"

"Pretty much," Theo answered. He thought for a second, then asked, "Why are you named 'Luke'? Do all Pokémon here have names?"

"Many of us respond to our species names, but yeah, we all have names. Makes it easy to identify us in the clan."

"Are you all Mudkip?"

"No, it's the whole genus. Mudkip, Marshtomp, and Swampert. We all live together to catch fish Pokémon and harvest berries and build huts and stuff. It's a nice place. You'll like it."

Theo looked uncomfortable. "Uh, you catch Pokémon..."

"Yeah. Magikarp mainly, but Tentacool every now and again. Finneon is a real treat, but they're rare in these parts."

"So you eat your fellow Pokémon?" Theo asked. "How do I know you're not leading me to your clan to, you know, eat me?"

Luke glanced back and laughed. "That's ridiculous! We only catch feral Pokémon. There's an underwater Mystery Dungeon just off the beach about a mile south of our community, so we fish up Pokémon from there. It's dangerous if you fall in, but it's an important job. Gotta eat some sort of meat for protein."

"What's a Mystery Dungeon?"

"Geez, Theo, you really do know nothing. I'll let the elder Swampert explain everything you need to know about, well, everything. He's REALLY wise, and maybe he knows something about how you became a Pokémon."

Theo shrugged. _It's worth a shot_ he thought to himself. _And he might know how I got turned into a Pokémon. And maybe I could get changed back!_

They walked for a few more minutes in silence, then Luke spoke up.

"We're here, Theo. This is my home."

Luke's home looked like a man-made – er – Pokémon-made wooden playground. Small wooden huts with leafy roofs were shoved almost anywhere there was space for them, including up in the air. Some were built up on platforms at varying heights, even on top of other huts, and were connected to each other by long planks, some wide enough for two Swampert to stand shoulder to shoulder, and some barely large enough to let baby Mudkip skitter across. Mudkip, Marshtomp, and the occasional Swampert populated the small city, wandering across the planks to other huts. Even the sandy ground was busy with the blue amphibious Pokémon. In the center of the village was a large fountain, launching water high into the air. The water appeared to sparkle with many colors in the receding sunlight.

"It's beautiful, isn't it?" Luke asked Theo.

"Yeah, it is. It feels very...homey."

"Yeah, it does..." Luke sighed, sounding both pleased and depressed.

Theo heard more depressed-sigh than pleased-sigh. "What's wrong, Luke?" he asked as they made their way towards the fountain. "This place is awesome!"

"Oh, nothing," Luke said. "I'm just tired. Long day today."

"I feel you. I think." Theo replied.

As they walked to the center of town, every clan member they passed stopped and stared at the orange lizard Pokémon.

"Uh, Luke," Theo said nervously. "Th-they're all staring at me."

"Don't worry about it. Charmander are very rare in these parts. The closest known Charmander village is at least a two-day hike through the forest. And we don't want to risk entering the Mystery Dungeon there by accident."

There was that word again. Mystery Dungeon. What were those? There seemed to be a few of these Mystery Dungeons by the village. That was one more thing to ask the elder Swampert about.

They arrived at the fountain. It was bigger and more beautiful up close. The sides of the fountain were made of sandstone and had ornate carvings all along it. There were four smaller streams of water, one in each cardinal direction, shooting into the sky along with the huge central water-pillar.

Walking to the other side of the fountain, Theo saw why this was their destination. Behind the fountain was a giant hole in the ground, with a ramp leading down into it. The entrance wasn't anything special, but something BIG must have been in here for the hole to be that size.

"This is where the elder Swampert lives," said Luke. "If you want to talk to him now, I can go see if he's available. I'm sure he'd be happy to speak to a Charmander-human-whatever." He chuckled.

"Uh, thanks, but I just want something to eat. Maybe after dinner."

"Sure thing," Luke said. "Let's go to my house. Mom's making Lum Berry stew tonight, and it's amazing!"

Luke's house was near the top of the village and was just like any other: small, wooden, and leafy, with openings in the walls to serve as windows. Being right by the fountain and the elder's quarters, it was a short walk for Luke but quite the climb for Theo.

He tried to speak, but was wheezing too much to say anything. Luke looked at him worryingly.

"It-it's okay, Luke," Theo managed to get out. "I guess I'm just not used to this body yet."

Luke laughed. "Oh yeah, I forgot about that. Let's get some of that stew inside that new body and see if that doesn't do you any good."

Luke's mother, a smaller Swampert, was surprised to see a Charmander enter their home and nearly exploded on Luke for bringing a Fire-type into the wooden hut. Luke explained how he found Theo on the beach and how he lost his memory, leaving out the fact that Theo was a human. She begrudgingly offered him a spot at the table and they ate in silence. After the meal, they headed back out to the elder's cave.

"The stew was delicious," Theo said. "Thanks for not telling her about me being a human. I'm not sure if that's a good thing or not here."

"Believe me, it's a cool thing for sure," Luke responded. "Humans are legendary, and we know almost nothing about them. Everyone will have so many questions for you about being a human! Is it true that humans could shrink any Pokémon to fit in a small ball?"

"What are you talking about? I don't remember anything, remember?"

Luke face-palmed...er...pawed? "Oh yeah, that."

They arrived at the sunken cave where the elder Swampert resides. Luke looked at Theo. "Wait right here. I'll see if the elder wants to see you."

Luke walked down the ramp and kept going down further than Theo could see. Five minutes passed. Ten. Fifteen.

Theo sat counting stars in the night sky when Luke became visible again. He was huffing as he reached the surface. Now it was Theo's turn to chuckle at his new acquaintance. "Not so easy for you to climb either, huh?"

"Shut up. This goes all the way down to the bedrock. It's a long walk down, and a longer walk back up. But yeah, the elder wants to see you now. I think he's excited to meet a human."

They started walking down the ramp into the elder's cavern. Water dripped from the ceiling and moistened the hard rock on the ground. The ramp began to spiral around to the left, and a faint roaring could be heard coming from the left wall. It sounded like water, but Theo couldn't be too sure.

"So," Theo asked, "has anyone here ever met a human before?"

"Not that I know of," Luke responded, "but if anyone's seen one, it's the elder. No one knows how old he is, so maybe he's met one!"

"Tell me more about this elder Swampert."

The whole way down, Luke talked about the elder as if he were a legend and listed off some of his accomplishments. How some said he was born a Swampert instead of a Mudkip, how he singlehandedly saved the village many years before Luke was born, how he used to head the greatest exploration team in the land before he retired to village life.

"What's an exploration team?" Theo asked. But as he finally got one question out to the rambling Mudkip, a large stone door appeared around the ramp's bend. The ramp straightened out and lead directly into the door.

"We're here!" Luke said excitedly. He ran up to the door and knocked on it. "I'm here, elder! I brought the Charmander!"

The entire cave started shaking. Theo shivered slightly out of nervousness. _What if the cave collapses on top of us? I didn't come here to die._ He almost turned to flee, but the door slowly opened for them to enter. The shaking stopped as the door clicked into place. It was wide open for the two Pokémon.

"Well, let's go in and get you some answers," Luke said. He skipped into the large room behind the door.

 _Yeah, hopefully I can get something out of this_ Theo thought as he followed Luke into the elder's main room.


End file.
